mcwdsi/bam2tensor: v2.0

Changes :boom: Breaking Changes 3.0: stricter call rules (proper pairs, intact CpG, base quality), reference check, review fixes (#99) @semenko One row per fragment: merge mates, decode both strands, record output format version (#96) @semenko :rocket: Features Warn when read bases contradict the aligner's strand tag (#98) @semenko :beetle: Fixes Atomic output files, exact CpG context for the non-converted filter, directional-library caveat (#97) @semenko One row per fragment: merge mates, decode both strands, record output format version (#96) @semenko Robustness fixes: clear errors, atomic writes, no silent filter no-ops; simulated-truth tests (#93) @semenko :racehorse: Performance Performance: compact extraction buffers, no per-position lookup table, cheaper cache checks (#95) @semenko :rotating_light: Testing Robustness fixes: clear errors, atomic writes, no silent filter no-ops; simulated-truth tests (#93) @semenko :construction_worker: Continuous Integration CI: per-ref concurrency, single-source uv/nox pins, ignore CpG caches (#92) @semenko :books: Documentation Atomic output files, exact CpG context for the non-converted filter, directional-library caveat (#97) @semenko :package: Dependencies Bump the uv-dependencies group with 4 updates (#94) @dependabot[bot], @semenko Bump the workflows-dependencies group in /.github/workflows with 2 updates (#89) @dependabot[bot] Bump the github-action-dependencies group with 3 updates (#90) @dependabot[bot] Bump the uv-dependencies group with 21 updates (#91) @dependabot[bot] Bump uv from 0.12.7 to 0.12.19 in /.github/workflows in the workflows-dependencies group (#87) @dependabot[bot] Bump the uv-dependencies group with 20 updates (#88) @dependabot[bot] Bump the uv-dependencies group with 45 updates (#86) @dependabot[bot] Bump the workflows-dependencies group in /.github/workflows with 2 updates (#85) @dependabot[bot] Bump the uv-dependencies group with 7 updates (#84) @dependabot[bot] Bump the github-action-dependencies group with 3 updates (#83) @dependabot[bot] Bump the workflows-dependencies group in /.github/workflows with 2 updates (#82) @dependabot[bot] Bump the uv-dependencies group with 4 updates (#81) @dependabot[bot] Bump the github-action-dependencies group with 4 updates (#80) @dependabot[bot] Bump the uv-dependencies group with 5 updates (#79) @dependabot[bot] Bump release-drafter/release-drafter from 7.2.1 to 7.3.1 in the github-action-dependencies group (#78) @dependabot[bot]